As the dominant mercury species in fish, methylmercury (MeHg) biomagnifies during its trophic transfer through aquatic food webs. MeHg is known to bind to cysteine, forming the complex of MeHg-cysteine. However, relationship between MeHg and cysteine in large-scale food webs has not been explored and contrasted with MeHg biomagnification models. Here, we quantified the compound-specific nitrogen isotopic analysis of amino acids (CSIA-AA), MeHg, and amino acid composition in aquatic organisms of Poyang Lake, the largest freshwater lake in China. The trophic positions (TPAA) of organisms ranged from 1.0 ± 0.1-3.7 ± 0.2 based on CSIA-AA approach. The trophic magnification factor (TMF) of MeHg, derived from the regression slope of Log-transformed MeHg in organisms upon their TPAA for the entire food web was 9.5 ± 0.5. Significantly positive regression between MeHg and cysteine (R2 = 0.64, p < 0.01) was documented, suggesting MeHg-cysteine complex may potentially play a critical role in the bioaccumulation of MeHg. Furthermore, TMFs of MeHg calculated with and without cysteine normalization compared well (7.7-8.7) when excluding primary producers. Our results implied that MeHg may biomagnify as the complex of MeHg-cysteine and contribute to our understanding of MeHg trophic transfer at the molecular level.